Journal of Biogeography
SUPPORTING INFORMATION
New insights into the evolutionary history of white sharks, Carcharodon carcharias
Sara Andreotti, Sophie von der Heyden, Romina Henriques, Michael Rutzen, Michael Meÿer, Herman Oosthuizen, Conrad A. Matthee
APPENDIX S1: (a) Photographic evidence of dorsal fins confirmed by genetic fingerprints that are identical and satellite telemetry evidences of the white
shark’s dispersal potential around southern Africa coastline. The correspondence between photo identification and the genetic fingerprint of a white shark
(3.7m Female) shows evidence of the reliability of the photographic identification to visually recognize the individuals (Figure S1a,b). For this study double
sampling the same animals was avoided, whenever possible, by visually comparing the dorsal fins.
Figure S1: The correspondence between photo identification, and the genetic fingerprint of a white shark (3.7m Female) shows evidence of the sharks’
movements across the coastline (a) Dorsal fin photo identification of the same shark sampled at Algoa Bay and False Bay; (b) Example of microsatellites
score with the software Geneious version 5.6.5 (© Biomatters Ltd.) of two samples belonging to the same shark; (c) Genotype identity between the two
samples; (d) satellite telemetry tracking of individual white sharks (each represented by a different colour) around southern Africa coastline, from the website:
http://www.ocearch.org/#SharkTracker.
APPENDIX S2: Microsatellites primers details, multiplex panels and annealing temperature.
MULTIPLEX PANEL
LOCUS
PRIMERS
Repeat
CCa1419
ATTATCGCATTGGGGGATTT
GCAGCAGTCACTCTTGGGTA
CCTTAAAAGCACAGAACAAAGATAAA
GGGGATTTACAGAGAGCATCC
ACTCCGGATTGGTGCTATTG
TTGGTCCTCCTTTGCTGAAT
Dyes
Range
[TG]13
6-FAM
150-190
[TAGA]16
VIC
185-220
[TG]19
NED
230-270
CCa1273
TGTTTTTGCCTTTTATCCTTGAA
CCAGAAACCCACCCAAGTAA
[TG]10
PET
165-195
Ccar1
GCAGAGGTTGGGAAAGAGTT
GCTATTCCAGTGACACTCTCC
GATGATTTTGCATGTCACTTTGA
CTTTGCCTAATATTATTGAGAGAT
CCCTGTGTTCTTGCACAATG
CCATTGAAGCCCTGTGAAGT
GAGCATGTGTGGGAGCGAAAG
TGGGACGATTCTGCCATTCTCTC
[AC]22
6-FAM
155-170
[CA]19
VIC
165-195
[AC]26
NED
190-240
NA
PET
165-186
ATGTGTGCAAGCAAGTCTGC
GCATAACACCCCCACAGAAG
CCTAGCATTATGGTCAACATCAG
GGTCACTTTCAACTTGAGCAAA
CTCTGGTTTCCTCCCAAGGT
CAGGAGATGGGCACTACACA
[TG]9[TG]11
6-FAM
230-250
[TG]21
VIC
155-195
[TG]12
PET
150-170
AGGAAATTAGGTGGGGAGGCAG
GCCAAATAGATTCTGTCCTTGACCC
AATGGGTTGTGATGGGAGTTT
CAAGTGGAAGTCAAGCAGGTT
GCTGAGTGCTGGCTGACCT
TATCCAGTTACCATCTCCAAAAA
[GA]18
6-FAM
110-130
[TG]23
NED
200-247
[TG]4TT[TG]9TT[TG]3TTTT[TG]23
PET
265-300
A
CCa83
CCa1536
Annealing
Temperature (°C)
50.0
Simplex
55.0
B
60.0
CCa711
CCa1072
Ccar6.27x
C
60.6
CCa1466
CCa1276
CCa1226
D
63.2
Iox10
Ccar9
Ccar13
APPENDIX S3: Nuclear genetic diversity of C. carcharias at 14 microsatellite loci per sampling site:
n – number of successfully genotyped individuals per locus; Na – number of alleles at each locus; HO
– observed heterozygosity; HE – expected heterozygosity; AR – allelic richness; FIS – Inbreeding
coefficient. Significant deviations from Hardy-Weinberg expectations, p<0.0001 after Bonferroni
correction, are indicated by a *.
Locus
Cca1419
Cca83
Cca1536
Cca1273
Ccar1
Cca711
Cca1072
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
Algoa Bay False Bay
Gansbaai
9
3
1
0.582
3
-0.800
9
5
1.000
0.752
4
-0.358
9
5
0.889
0.719
11
-0.255
9
2
0.333
0.503
3
0.351
9
4
0.889
0.732
5
-0.231
9
5
0.556
0.641
7
0.111
9
5
0.556
0.667
20
167
3
1
0.519
3
-0.933
167
7
0.784
0.794
8
0.012
167
7
0.850
0.807
11
-0.053
167
2
0.419
0.443
3
0.054
167
6
0.743
0.696
5
-0.067
167
7
0.563
0.540
10
-0.050
167
8
0.689
0.815
20
11
3
1
0.567
3
-0.833
11
5
0.818
0.792
4
-0.034
11
7
0.818
0.840
11
0.027
11
2
0.364
0.416
3
0.130
11
4
0.909
0.710
5
-0.299
11
5
0.727
0.680
7
-0.143
11
8
0.727
0.857
20
Struisbaai
De Hoop
18
3
1
0.586
3
-0.744
18
6
0.889
0.706
7
-0.268
18
6
0.944
0.783
11
-0.214
18
2
0.611
0.437
3
-0.417
18
4
0.778
0.624
5
-0.256
18
6
0.611
0.638
10
-0.067
18
7
0.722
0.775
20
Mossel Bay Overall
28
3
1
0.527
3
-0.931
28
7
0.786
0.820
8
0.043
28
7
0.786
0.825
11
0.048
28
2
0.571
0.486
3
-0.180
28
5
0.607
0.700
5
0.135
28
5
0.464
0.534
10
0.091
28
8
0.750
0.810
20
233
3
1.000
0.526
3
-0.906
233
7
0.803
0.789
6.2
-0.017
233
7
0.850
0.808
11
-0.051
233
2
0.446
0.446
3
0
233
6
0.742
0.691
5
-0.075
233
9
0.562
0.556
8.8
-0.036
233
8
0.695
0.807
20
Ccar627.x
Cca1466
Cca1276
Cca1226
Iox10
Ccar9
Ccar13
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
n
Na
Ho
He
AR
FIS
0.175
9
3
0.667
0.621
4
-0.079
9
2
0.333
0.294
1
-0.143
9
7
0.778
0.843
13
0.082
9
3
0.556
0.464
5
-0.212
8
4
0.750
0.742
4
-0.012
8
7
0.750
0.800
11
0.067
8
3
0.750
0.667
2
0.056
0.158
11
2
0.182
0.173
4
-0.053
11
2
0.636
0.455
1
-0.429
11
6
1.000
0.836
5
-0.209
11
2
0.455
0.455
3
0.000
10
4
0.500
0.647
4
0.237
9
8
0.889
0.797
12
-0.123
8
3
0.750
0.633
2
-0.012
0.155*
167
3
0.461
0.452
4
-0.020
162
3
0.457
0.358
2
-0.276
163
16
0.933
0.874
15
-0.067
163
5
0.264
0.291
5
0.094
155
5
0.671
0.673
5
0.003
156
15
0.750
0.831
19
0.098*
148
3
0.696
0.595
2
-0.061
0.069
18
3
0.611
0.538
4
-0.140
18
2
0.278
0.246
1
-0.133
18
10
0.833
0.870
14
0.043
18
4
0.333
0.340
5
0.019
15
5
0.867
0.786
5
-0.106
15
10
0.733
0.862
13
0.154
12
3
0.667
0.627
2
-0.126
0.076
28
3
0.643
0.515
4
-0.254
26
3
0.538
0.419
2
-0.292
25
9
0.880
0.856
14
-0.029
26
4
0.346
0.389
5
0.112
26
5
0.615
0.626
5
0.017
25
12
0.880
0.832
14
-0.059
21
3
0.714
0.664
2
-0.071
0.139*
233
3
0.489
0.464
4
-0.054
226
3
0.456
0.358
1.4
-0.274
226
16
0.916
0.867
12.2
-0.057
227
5
0.299
0.322
4.6
0.069
214
5
0.673
0.677
4.6
0.006
213
15
0.770
0.828
13.8
0.07
197
9
0.701
0.607
2
-0.06
APPENDIX S4
Table S4: List of species, nucleotide (π) and haplotype (h) diversity and reference used to plot
marine organism diversity value in Fig. S4.
SPECIES
π
h
REFERENCE
Sharks
Charcharodon carcharias SA
Charcharodon carcharias AU
Carcharodon carcharias CA
Cetorhinus maximus
Carcharhinus limbatus
Carcharias taurus
Sphyrna lewini
Carcharinus leucas
0.003
0.007
0.001
0.001
0.002
0.003
0.013
0.003
0.205
0.868
0.660
0.720
0.805
0.717
0.800
0.760
This study
Blower et al., 2012
Jorgensen et al., 2010
Hoelzel et al., 2006
Keeney et al., 2005
Stow et al., 2006
Duncan et al., 2006
Karl et al., 2011
Marine Mammals
Physeter macrocephalus
Orcinus orca
Tursiops truncatus
Delphinus delphis
0.002
0.005
0.013
0.012
0.860
0.874
0.420
0.853
Lyrholm et al., 1996
Hoelzel et al., 2002
Natoli et al., 2005
Natoli et al., 2006
Marine teleostei SA
Clinus cottoides
Hippocampus capensis
Merluccius capensis
Merluccius paradoxus
Rhabdosargus holubii
Caffrogobius caffer
Argyrosomus japonicus
0.003
0.004
0.006
0.001
0.006
0.002
0.009
0.660
0.780
0.880
0.530
0.910
0.960
0.960
von der Heyden et al., 2008
Teske et al., 2003
von der Heyden et al., 2007
von der Heyden et al., 2010
Oosthuizen, 2007
Neethling et al., 2008
Klopper, 2005
Marine teleostei
Merluccius australis
Lophius piscatorius
Lophius budegassa
Cynoscion acoupa
Girella punctata
Acanthocybium solandri
Lateolabrax japonicus
Trachurus trachurus
Lateolabrax maculates
Ocyurus chrysurus
Aphanopus carbo
Helicolenus dactylopterus
Scomber scombrus
Pagrus pagrus
Centropyge spp.
Latris lineata
0.002
0.008
0.009
0.003
0.009
0.006
0.003
0.009
0.012
0.019
0.019
0.005
0.029
0.011
0.022
0.040
0.470
0.770
0.880
0.890
0.910
0.920
0.960
0.960
0.960
0.960
0.970
0.980
0.990
0.990
0.990
0.990
Machado-Schiaffino et al., 2009
Charrier et al., 2006
Charrier et al., 2006
Rodrigues et al., 2008
Umino et al., 2009
Theisen et al., 2008
Liu et al., 2006
Comesaña et al., 2008
Liu et al., 2006
Vasconcellos et al., 2008
Stefanni & Knutsen, 2007
Aboim et al., 2005
Nesbo et al., 2000
Ball et al., 2007
Bowen et al., 2006
Tracey et al., 2007
Figure S4 Graph showing mtDNA nucleotide and haplotype diversity for a range of marine organism (see
Table 5 for species and references). South African species are indicated in red, white sharks are indicated by
“■”.
REFERENCES TABLE S4
Aboim, M.A., Menezes G.M., Schlitt T., & Rogers A.D. (2005) Genetic structure and history of populations
of the deep-sea fish Helicolenus dactylopterus (Delaroche, 1809) inferred from mtDNA sequence
analysis. Molecular Ecology, 14, 1343–1354.
Ball, A.O., Beal M.G., Chapman R.W., & Sedberry G.R. (2007) Population structure of red porgy, Pagrus
pagrus, in the Atlantic Ocean. Marine Biology, 150, 1321–1332.
Blower, D., Pandolfi J., Bruce B., Gomez-Cabrera M., & Ovenden J. (2012) Population genetics of Australian
white sharks reveals fine-scale spatial structure, transoceanic dispersal events and low effective
population sizes. Marine Ecology Progress Series, 455, 229–244.
Bowen, B.W., Muss A., Rocha L.A., & Grant W.S. (2006) Shallow mtDNA coalescence in Atlantic pygmy
angelfishes (genus Centropyge) indicates a recent invasion from the Indian Ocean. Journal of
Heredity, 97, 1–12.
Charrier, G., Chenel T., Durand J.D., Girard M., Quiniou L., & Laroche J. (2006) Discrepancies in
phylogeographical patterns of two European anglerfishes (Lophius budegassa and Lophius
piscatorius). Molecular Phylogenetics and Evolution, 38, 742–754.
Comesaña, A.S., Martínez-Areal M.T., & Sanjuan A. (2008) Genetic variation in the mitochondrial DNA
control region among horse mackerel (Trachurus trachurus) from the Atlantic and Mediterranean
areas. Fisheries Research, 89, 122–131.
Duncan, K.M., Martin A.P., Bowen B.W., & De Couet H.G. (2006) Global phylogeography of the scalloped
hammerhead shark (Sphyrna lewini). Molecular Ecology, 15, 2239–2251.
Von der Heyden, S., Lipinski M.R., & Matthee C.A. (2007) Mitochondrial DNA analyses of the Cape hakes
reveal an expanding, panmictic population for Merluccius capensis and population structuring for
mature fish in Merluccius paradoxus. Molecular Phylogenetics and Evolution, 42, 517–527.
Von der Heyden, S., Lipinski M.R., & Matthee C.A. (2010) Remarkably low mtDNA control region diversity
in an abundant demersal fish. Molecular Phylogenetics and Evolution, 55, 1183–1188.
Von der Heyden, S., Prochazka K., & Bowie R.C.K. (2008) Significant population structure and asymmetric
gene flow patterns amidst expanding populations of Clinus cottoides (Perciformes, Clinidae):
application of molecular data to marine conservation planning in South Africa. Molecular Ecology,
17, 4812–4826.
Hoelzel, A.R., Natoli A., Dahlheim M.E., Olavarria C., Baird R.W., & Black N.A. (2002) Low worldwide
genetic diversity in the killer whale (Orcinus orca): implications for demographic history.
Proceedings of the Royal Society of London. Series B: Biological Sciences, 269, 1467–1473.
Hoelzel, A.R., Shivji M.S., Magnussen J., & Francis M.P. (2006) Low worldwide genetic diversity in the
basking shark (Cetorhinus maximus). Biology Letters, 2, 639–642.
Jorgensen, S.J., Reeb C.A., Chapple T.K., Anderson S., Perle C., Van Sommeran S.R., Fritz-Cope C., Brown
A.C., Klimley A.P., & Block B.A. (2010) Philopatry and migration of Pacific white sharks.
Proceedings of the Royal Society B: Biological Sciences, 277, 679–688.
Karl, S.A., Castro A.L.F., Lopez J.A., Charvet P., & Burgess G.H. (2011) Phylogeography and conservation
of the bull shark (Carcharhinus leucas) inferred from mitochondrial and microsatellite DNA.
Conservation Genetics, 12, 371–382.
Keeney, D.B., Heupel M.R., Hueter R.E., & Heist E.J. (2005) Microsatellite and mitochondrial DNA analyses
of the genetic structure of blacktip shark (Carcharhinus limbatus) nurseries in the northwestern
Atlantic, Gulf of Mexico, and Caribbean Sea. Molecular Ecology, 14, 1911–1923.
Klopper, A.W. (2005) Intraspecific genetic variation in the percoid teleosts, Argyrosomus japonicus
(Temminck & Schlegel, 1843) and Pomadasys commersonnii (Lacepede, 1801) as inferred from the
mitochondrial control region. University of Pretoria, South Africa.
Liu, J.-X., Gao T.-X., Yokogawa K., & Zhang Y.-P. (2006) Differential population structuring and
demographic history of two closely related fish species, Japanese sea bass (Lateolabrax japonicus)
and spotted sea bass (Lateolabrax maculatus) in Northwestern Pacific. Molecular Phylogenetics and
Evolution, 39, 799–811.
Lyrholm, T., Leimar O., & Gyllensten U. (1996) Low diversity and biased substitution patterns in the
mitochondrial DNA control region of sperm whales: implications for estimates of time since common
ancestry. Molecular Biology and Evolution, 13, 1318–1326.
Machado-Schiaffino, G., Campo D., & Garcia-Vazquez E. (2009) Strong genetic differentiation of the Austral
hake (Merluccius australis) across the species range. Molecular Phylogenetics and Evolution, 53,
351–356.
Natoli, A., Birkun A., Aguilar A., Lopez A., & Hoelzel A.R. (2005) Habitat structure and the dispersal of
male and female bottlenose dolphins (Tursiops truncatus). Proceedings of the Royal Society B:
Biological Sciences, 272, 1217–1226.
Natoli, A., Canadas A., Peddemors V.M., Aguilar A., Vaquero C., Fernandez-Piqueras P., & Hoelzel A.R.
(2006) Phylogeography and alpha taxonomy of the common dolphin (Delphinus sp.). Journal of
Evolutionary Biology, 19, 943–954.
Neethling, M., Matthee C.A., Bowie R.C., & von der Heyden S. (2008) Evidence for panmixia despite barriers
to gene flow in the southern African endemic, Caffrogobius caffer (Teleostei: Gobiidae). BMC
Evolutionary Biology, 8, 325.
Nesbo, C.L., Rueness E.K., Iversen S.A., Skagen D.W., & Jakobsen K.S. (2000) Phylogeography and
population history of Atlantic mackerel (Scomber scombrus L.): a genealogical approach reveals
genetic structuring among the eastern Atlantic stocks. Proceedings of the Royal Society B: Biological
Sciences, 267, 281–292.
Oosthuizen, C.J. (2007) Genetic variation within the cape stumpnose,
Steindachner(Teleostei: Sparidae). University of Pretoria, South Africa.
Rhabdosargus
holubi
Rodrigues, R., Schneider H., Santos S., Vallinoto M., Sain-Paul U., & Sampaio I. (2008) Low levels of
genetic diversity depicted from mitochondrial DNA sequences in a heavily exploited marine fish
(Cynoscion acoupa, Sciaenidae) from the Northern coast of Brazil. Genetics and Molecular Biology,
31, 487–492.
Stefanni, S. & Knutsen H. (2007) Phylogeography and demographic history of the deep-sea fish Aphanopus
carbo (Lowe, 1839) in the NE Atlantic: Vicariance followed by secondary contact or speciation?
Molecular Phylogenetics and Evolution, 42, 38–46.
Stow, A., Zenger K., Briscoe D., Gillings M., Peddemors V., Otway N., & Harcourt R. (2006) Isolation and
genetic diversity of endangered grey nurse shark (Carcharias taurus) populations. Biology Letters, 2,
308–311.
Teske, P.R., Cherry M.I., & Matthee C.A. (2003) Population genetics of the endangered Knysna seahorse,
Hippocampus capensis. Molecular Ecology, 12, 1703–1715.
Theisen, T.C., Bowen B.W., Lanier W., & Baldwin J.D. (2008) High connectivity on a global scale in the
pelagic wahoo, Acanthocybium solandri (tuna family Scombridae). Molecular Ecology, 17, 4233–
4247.
Tracey, S.R., Smolenski A., & Lyle J.M. (2007) Genetic structuring of Latris lineata at localized and
transoceanic scales. Marine Biology, 152, 119–128.
Umino, T., Kajihara T., Shiozaki H., Ohkawa T., Jeong D.-S., & Ohara K. (2009) Wild stock structure of
Girella punctata in Japan revealed shallow genetic differentiation but subtle substructure in subsidiary
distributions. Fisheries Science, 75, 909–919.
Vasconcellos, A.V., Vianna P., Paiva P.C., Schama R., & Solé-Cava A. (2008) Genetic and morphometric
differences between yellowtail snapper (Ocyurus chrysurus, Lutjanidae) populations of the tropical
West Atlantic. Genetics and Molecular Biology, 31: 308-316.